Comparative genomics of clinicalStenotrophomonas maltophiliaisolates reveals regions of diversity which correlate with colonization and persistence in vivo

Abstract

ABSTRACTStenotrophomonas maltophiliais a Gram-negative emerging opportunistic pathogen often found in respiratory diseases such as cystic fibrosis (CF). Patients with CF experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed thatP. aeruginosapromotes persistence ofS. maltophiliamouse respiratory infections. As is typical for environmental opportunistic pathogens,S. maltophiliahas a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content ofS. maltophilia,combining short and long read sequencing to construct complete genomes of 10 clinical isolates which were then compared with the larger phylogeny ofS. maltophiliagenomic sequence data, and compared colonization/persistence in vivo, alone and in coinfection withP. aeruginosa. We found that while the overall genome size and GC content were fairly consistent, there was considerable variability in arrangement and gene content. Similarly, there was significant variability inS. maltophiliacolonization and persistence in vivo in experimental mouse respiratory infection. Ultimately, this study gives us a greater understanding of the genomic diversity ofS. maltophiliaisolated from patients, and how this genomic diversity relates to interactions with other pulmonary pathogens, and to host disease progression. Identifying the molecular determinants of infection withS. maltophiliacan facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.